# This file is a slightly modified version of the document: # http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=t#SG4 # The modifications are mostly the removal of the 'i' indicating an initiator # and the introduction of '#'s to indicate comments. # The label to be used internally has also been added just after the # NCBI table identifier line, for brevity. #1. The Standard Code (transl_table=1) Label Standard TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA *Ter TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #AUG #Alternative Initiation Codons #(Prats et al. 1989; Hann et al. 1992) # #CUG, UUG #2. The Vertebrate Mitochondrial Code (transl_table=2) Label Vert_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA MMet ACA TThr AAA KLys AGA *Ter ATG MMet ACG TThr AAG KLys AGG *Ter GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # Code 2 Standard # AGA Ter * Arg R # AGG Ter * Arg R # AUA Met M Ile I # UGA Trp W Ter * # #Alternative Initiation Codon: # #Bos: AUA #Homo: AUA, AUU #Mus: AUA, AUU, AUC #Coturnix, Gallus: also GUG (Desjardins and Morais, 1991) # #Systematic Range: # #Vertebrata # #Comment: # #*The transcripts of several vertebrate mitochondrial genes end in U or UA, #which become termination codons (UAA) upon subsequent polyadenylation. #3. The Yeast Mitochondrial Code (transl_table=3) Label Yeast_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT TThr CCT PPro CAT HHis CGT RArg CTC TThr CCC PPro CAC HHis CGC RArg CTA TThr CCA PPro CAA QGln CGA RArg CTG TThr CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA MMet ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 3 Standard # # AUA Met M IIle I # CUU Thr T Leu L # CUC Thr T Leu L # CUA Thr T Leu L # CUG Thr T Leu L # UGA Trp W Ter * # # CGA absent Arg R # CGC absent Arg R # #Systematic Range: # #Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, #Schizosaccharomyces pombe, and Kluyveromyces thermotolerans (Clark-Walker #and Weiller, 1994) # #Comments: # #*The remaining CGN codons are rare in Saccharomyces cerevisiae and absent #in Candida glabrata (= Torulopsis glabrata). # #*The AUA codon is common in the gene var1 coding for the single #mitochonLIial ribosomal protein, but rare in genes encoding the enzymes. # #*The coding assignments of the AUA (Met or Ile) and CUU (possibly Leu, not #Thr) are uncertain in Hansenula saturnus. # #*The codon UGA is rarely used and probably encodes Trp in #Schizosaccharomyces pombe. Sequence comparisons do not suggest other #nonstandard codon assignments in this species. # #*The coding assignment of Thr to CUN is uncertain in Kluyveromyces #thermotolerans Clark-Walker and Weiller, 1994). #4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4) Label Mold_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 4 Standard # # UGA Trp W Ter * # #Alternative Initiation Codons: # #Trypanosoma: UUA, UUG, CUG #Leishmania: AUU, AUA #Tertrahymena: AUU, AUA, AUG #Paramecium: AUU, AUA, AUG, AUC, GUG, GUA(?) #(Pritchard et al., 1990) # #Systematic Range: # #Mycoplasmatales: Mycoplasma, Spiroplasma (Bove et al., 1989); # #Fungi: Emericella nidulans, Neurospora crassa, Podospora anserina, #Acremonium (Fox, 1987), Candida parapsilosis (Guelin et al., 1991), #Trichophyton rubrum (de Bievre and Dujon, 1992), Dekkera/Brettanomyces, #Eeniella (Hoeben et al., 1993), and probably Ascobolus immersus, Aspergillus #amstelodami, Claviceps purpurea, and Cochliobolus heterostrophus. # #Protozoa: Trypanosoma brucei, Leishmania tarentolae, Paramecium tetraurelia, #Tetrahymena pyriformis and probably Plasmodium gallinaceum (Aldritt et al., #1989)]. # #Metazoa: Coelenterata (Ctenophora and Cnidaria) # #Comments: # # * This code is also used for the kinetoplast DNA (maxicircles, # minicircles). Kinetoplasts are modified mitochondria (or their parts). # # * This code is not used in the Acholeplasmataceae and plant-pathogenic # mycoplasma-like organisms (MLO) (Lim and Sears, 1992) #5. The Invertebrate Mitochondrial Code (transl_table=5) Label Invert_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA MMet ACA TThr AAA KLys AGA SSer ATG MMet ACG TThr AAG KLys AGG SSer GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Comment: # #The codon AGG is absent in Drosophila. # #Differences from the Standard Code: # # Code 5 Standard # # AGA Ser S Arg R # AGG Ser S Arg R # AUA Met M Ile I # UGA Trp W Ter * # #Alternative Initiation Codons: # #AUA, AUU #AUC: Apis (Crozier and Crozier, 1993) #GUG: Polyplacophora (Boore and Brown, 1994) #UUG: Ascaris, Caenorhabditis # #Systematic Range: # #Nematoda: Ascaris, Caenorhabditis; #Mollusca: Bivalvia (Hoffmann et al., 1992); Polyplacophora (Boore and Brown, #1994) #Arthropoda/Crustacea: Artemia (Batuecas et al., 1988); #Arthropoda/Insecta: Drosophila [Locusta migratoria (migratory locust), Apis #mellifera (honeybee)] # #Comments: # # * GUG may possibly function as an initiator in Drosophila (Clary and # Wolstenholme, 1985; Gadaleta et al., 1988). AUU is not used as an # initiator in Mytilus (Hoffmann et al., 1992). # # * "An exceptional mechanism must operate for initiation of translation of # the cytochrome oxidase subunit mRNA in both D. melanogaster (de # Bruijn, 1983) and D. yakuba (Clary and Wolstenholme 1983), since its # only plausible initiation codon, AUA, is out of frame with the rest of # the gene. Initiation appears to require the "reading" of of an AUAA # quadruplet, which would be equivalent to initiation at AUA followed # immediately by a specific ribosomal frameshift. Another possible # mechanism ... is that the mRNA is "edited" to bring the AUA initiation # into frame." (Fox, 1987) #6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6) Label Ciliate_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA QGln TGA *Ter TTG LLeu TCG SSer TAG QGln TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 6 Standard # # UAA Gln Q Ter * # UAG Gln Q Ter * # #Systematic Range: # #Ciliata: Oxytricha and Stylonychia (Hoffman et al. 1995), Paramecium, #Tetrahymena, Oxytrichidae and probably Glaucoma chattoni. # #Dasycladaceae: Acetabularia (Schneider et al., 1989) and Batophora #(Schneider and de Groot, 1991). # #Diplomonadida: #Scope: Hexamita inflata, Diplomonadida ATCC50330, and ATCC50380. #Ref.: Keeling, P.J. and Doolittle, W.F. 1996. A non-canonical genetic code #in an early diverging eukaryotic lineage. The EMBO Journal 15, 2285-2290. # #Comment: # # * The ciliate macronuclear code has not been determined completely. The # codon UAA is known to code for Gln only in the Oxytrichidae. # # ------------------------------------------------------------------------ # #Tables 7 and 8 have been deleted #9. The Echinoderm Mitochondrial Code (transl_table=9) Label Echino_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA NAsn AGA SSer ATG MMet ACG TThr AAG KLys AGG SSer GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 9 Standard # # AAA Asn N Lys K # AGA Ser S Arg R # AGG Ser S Arg R # UGA Trp W Ter * # #Systematic Range: # #Asterozoa (starfishes) (Himeno et al., 1987) Echinozoa (sea urchins) (Jacobs #et al., 1988; Cantatore et al., 1989) #10. The Euplotid Nuclear Code (transl_table=10) Label Euplotid_Nuclear TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA CCys TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 10 Standard # # UGA Cys C Ter * # #Systematic Range: # #Ciliata: Euplotidae (Hoffman et al. 1995). #11. The Bacterial "Code" (transl_table=11) Label Bacterial TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA *Ter TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # #None # #Alternative Initiation Codons: # #GUG, UUG, AUU, CUG # #Systematic Range: # #Prokaryotes including the eubacteria (Kozak, 1983) and archaebacteria (Brown #et al. 1989; Noelling et al., unpublished). # #Comments: # # * UGA codes at low efficiency for Trp in Bacillus subtilis and, # presumably, in Escherichia coli (Hatfiled and Diamond, 1993). # # * CUG is known to function as an initiator for one plasmid-encoded # protein (RepA) in Escherichia coli (Spiers and Bergquist, 1992) and # possibly in Methanobacterium thermoautotrophicum (Noelling et al., # unpublished) # # * There is no record of AUU initition codon for the archaebacteria. #12. The Alternative Yeast Nuclear Code (transl_table=12) Label Alt_Yeast TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA *Ter TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG SSer CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 12 Standard # # CUG Ser Leu # # #Alternative Initiation Codons: # #CAG may be used in Candida albicans (Santos et al., 1993). # #Systematic Range: # #Endomycetales (yeasts): Candida albicans, Candida cylindracea, Candida #melibiosica, Candida parapsilosis, and Candida rugosa (Ohama et al., 1993). # #Comment: # # * However, other yeast, including Saccharomyces cerevisiae, Candida # azyma, Candida diversa, Candida magnoliae, Candida rugopelliculosa, # Yarrowia lipolytica, and Zygoascus hellenicus, definitely use the # standard (nuclear) code (Ohama et al., 1993). #13. The Ascidian Mitochondrial Code (transl_table=13) Label Ascidian_Mito TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA MMet ACA TThr AAA KLys AGA GGly ATG MMet ACG TThr AAG KLys AGG GGly GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 13 Standard # # AGA Gly G Arg R # AGG Gly G Arg R # AUA Met M IIle I # UGA Trp W Ter * # #Systematic Range: # #Ascidiacea (sea squirts): Pyuridae (Durrheim et al. 1993; Yokobori et al., #1993) #14. The Flatworm Mitochondrial Code (transl_table=14) Label Flatworm TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA YTyr TGA WTrp TTG LLeu TCG SSer TAG *Ter TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA NAsn AGA SSer ATG MMet ACG TThr AAG KLys AGG SSer GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 14 Standard # # AAA Asn N Lys K # AGA Ser S Arg R # AGG Ser S Arg R # UAA Tyr Y Ter * # UGA Trp W Ter * # #Systematic Range: # #Platyhelminthes (flatworms) #15. Blepharisma Nuclear Code (transl_table=15) Label Blepharisma TTT FPhe TCT SSer TAT YTyr TGT CCys TTC FPhe TCC SSer TAC YTyr TGC CCys TTA LLeu TCA SSer TAA *Ter TGA *Ter TTG LLeu TCG SSer TAG QGln TGG WTrp CTT LLeu CCT PPro CAT HHis CGT RArg CTC LLeu CCC PPro CAC HHis CGC RArg CTA LLeu CCA PPro CAA QGln CGA RArg CTG LLeu CCG PPro CAG QGln CGG RArg ATT IIle ACT TThr AAT NAsn AGT SSer ATC IIle ACC TThr AAC NAsn AGC SSer ATA IIle ACA TThr AAA KLys AGA RArg ATG MMet ACG TThr AAG KLys AGG RArg GTT VVal GCT AAla GAT DAsp GGT GGly GTC VVal GCC AAla GAC DAsp GGC GGly GTA VVal GCA AAla GAA EGlu GGA GGly GTG VVal GCG AAla GAG EGlu GGG GGly #Differences from the Standard Code: # # Code 10 GStandard # #UAG Gln Q Ter * # #Systematic Range: # #Ciliata: Blepharisma (Liang and Heckman, 1993) # # ------------------------------------------------------------------------ # # Other Alternative Initiation Codons # # ------------------------------------------------------------------------ # # * GUG, UUG (and possibly CUG) in the Archaea (Noelling et al., # unpublished) # # * AUA, GUG, UUG, and AUC or AAG may be used (at least in experimental # systems) by the yeasts Saccharomyces cerevisiae (Olsen, 1987, and # references therein). # # * ACG initiates translation of certain proteins in the adeno-associated # virus type 2 (Becerra et al., 1985), the phage T7 mutant CR17 (Anderson # and Buzash-Pollert, 1985), Sendai virus (Gupta and Patwardhan, 1988), # and rice chloroplast (Hiratsuka et al., 1989). Also, it is the most # effective non-AUG initiation codon in mammalin cells (Koepke and # Leggatt, 1991). # # * CUG is the initiation codon for one of the two alternative products of # the human c-myc gene (Hann et al., 1987). # # ------------------------------------------------------------------------ # # Cited References # # ------------------------------------------------------------------------ # #Aldritt, S.M., Joseph, J.T., and Wirth, D.F. (1989) Mol. Cell. Biol. 9, #3614-3620. # #Anderson, C.W. and Buzash-Pollert, E. (1985) Mol. Cell. Biol. 5, 3621-3624. # #Batuecas, B., Garesse, R., Calleja, M., Valverde, J.R., and Marco, R. (1988) #Nucleic Acids Res. 16, 6515-6529. # #Becerra, S.P., Rose, J.A., Hardy, M., Baroudy, B.M., and Anderson, C.W. #(1985) Proc. Natn. Acad. Sci. USA 82: 7919-7923. # #Boore, J. L. and Brown, W. M. (1994) (GenBank Accession Number: U09810). # #Bove, J.M. Carle, P., Garnier, M., Laigret, F., Renaudin, J., and Saillard, #C. (1989) in The Mycoplasmas, R.F. 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